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Fundamental and Computational Sciences Directorate

Staff information

Carrie Nicora

Metabolomics
Chemist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352

PNNL Publications

2018

  • Menachery V.D., A. Schafer, K.E. Burnum-Johnson, H.D. Mitchell, A.J. Eisfeld-Fenney, K.B. Walters, and C.D. Nicora, et al. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115, no. 5:E1012-E1021. PNNL-SA-126254. doi:10.1073/pnas.1706928115
  • Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
  • Wu J., A. Sabag-Daigle, M. Borton, L. Kop, B.E. Szkoda, B. Kaiser, and S.R. Lindemann, et al. 2018. "Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut." Infection and Immunity 86, no. 7:e00945-17. PNNL-SA-129012. doi:10.1128/IAI.00945-17

2017

  • Boenisch M.J., K.L. Broz, S.O. Purvine, W.B. Chrisler, C.D. Nicora, L. Connolly, and M. Freitag, et al. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7. PNNL-SA-125650. doi:10.1038/srep44296
  • Booker A.E., M. Borton, R. Daly, S. Welch, C.D. Nicora, D.W. Hoyt, and T. Wilson, et al. 2017. "Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales." mSphere 2. PNNL-SA-128950. doi:10.1128/mSphereDirect.00257-17
  • Bryant A., M.J. Aldape, C.R. Bayer, E.J. Katahira, L. Bond, C.D. Nicora, and T.L. Fillmore, et al. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12, no. 12:Article No. e0172486. PNNL-SA-112551. doi:10.1371/journal.pone.0172486
  • Burnum-Johnson K.E., J.E. Kyle, A.J. Eisfeld, C.P. Casey, K.G. Stratton, J.F. Gonzalez, and F. Habyarimana, et al. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142, no. 3:442-448. PNNL-SA-116063. doi:10.1039/c6an02486f
  • Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
  • Li M., Y. Gao, W. Qian, L. Shi, Y. Liu, W.C. Nelson, and C.D. Nicora, et al. 2017. "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes." Environmental Microbiology Reports 9, no. 5:512-521. PNNL-SA-120732. doi:10.1111/1758-2229.12558
  • Liberton M.L., W.B. Chrisler, C.D. Nicora, R.J. Moore, R.D. Smith, D.W. Koppenaal, and H.B. Pakrasi, et al. 2017. "Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis sp. PCC 6803." PLoS One 12, no. 3:e0173251. PNNL-SA-112677. doi:10.1371/journal.pone.0173251
  • Shi T., S. Quek, Y. Gao, C.D. Nicora, S. Nie, T.L. Fillmore, and T. Liu, et al. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8, no. 60:101887-101898. PNNL-SA-128413. doi:10.18632/oncotarget.21710
  • Solden L., D.W. Hoyt, W.B. Collins, J.E. Plank, R. Daly, E. Hildebrand, and T.J. Beavers, et al. 2017. "New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11." The ISME Journal 11, no. 3:691-703. PNNL-SA-115562. doi:10.1038/ismej.2016.150

2016

  • Ahmad R., C.D. Nicora, A.K. Shukla, R.D. Smith, W. Qian, and A.Y. Liu. 2016. "An efficient method for native protein purification in the selected range from prostate cancer tissue digests." Chinese Clinical Oncology 5, no. 6:78. PNNL-SA-123158. doi:10.21037/cco.2016.12.03
  • Hiras J., Y. Wu, K. Deng, C.D. Nicora, J.T. Aldrich, D. Frey, and S. Kolinko, et al. 2016. "Comparative community proteomics demonstrates the unexpected importance of an actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis." mBio 7, no. 4:Article No. e01106-16. PNNL-SA-120275. doi:10.1128/mBio.01106-16
  • Khadempour L., K.E. Burnum-Johnson, E.S. Baker, C.D. Nicora, B.M. Webb-Robertson, R.A. White, and M.E. Monroe, et al. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25, no. 22:5795-5805. PNNL-SA-113016. doi:10.1111/mec.13872
  • Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
  • Pomraning K.R., Y. Kim, C.D. Nicora, R.K. Chu, E.L. Bredeweg, S.O. Purvine, and D. Hu, et al. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17, no. 138:1-18. PNNL-SA-112784. doi:10.1186/s12864-016-2471-2
  • Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891
  • Sigdel T.K., Y. Gao, J. He, A. Wang, C.D. Nicora, T.L. Fillmore, and T. Shi, et al. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury." Kidney International 89, no. 6:1244-1252. PNNL-SA-115293. doi:10.1016/j.kint.2015.12.049
  • Smith D., C.D. Nicora, P. Carini, M.S. Lipton, A.D. Norbeck, R.D. Smith, and S.J. Giovannoni. 2016. "Proteome Remodeling in Response to Sulfur Limitation in “Candidatus Pelagibacter ubique”." mSystems 1, no. 4:e00068-16. PNNL-SA-113512. doi:10.1128/mSystems.00068-16
  • Sun J., J.D. Todd, J. Thrash, Y. Qian, M.C. Qian, B. Temperton, and J. Guo, et al. 2016. "The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol." Nature Microbiology 1, no. 8:Article No. 16065. PNNL-SA-108154. doi:10.1038/nmicrobiol.2016.65
  • Tisoncik-Go J., D.J. Gasper, J.E. Kyle, A.J. Eisfeld, C. Selinger, M. Hatta, and J. Morrison, et al. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19, no. 2:254-66. PNWD-SA-10483. doi:10.1016/j.chom.2016.01.002
  • Walker L.R., D.W. Hoyt, S. Walker, J.K. Ward, C.D. Nicora, and A.K. Bingol. 2016. "Unambiguous Metabolite Identification in High-throughput Metabolomics by Hybrid 1D 1H NMR/ESI MS1 Approach." Magnetic Resonance in Chemistry 54, no. 12:998-1003. PNNL-SA-117020. doi:10.1002/mrc.4503
  • White R.A., E.M. Bottos, T. Roy Chowdhury, J.D. Zucker, C.J. Brislawn, C.D. Nicora, and S.J. Fansler, et al. 2016. "Moleculo long-read sequencing facilitates assembly and resolves functionally active genomic bins from complex soil metagenomes." mSystems 1, no. 3. PNNL-SA-117268. doi:10.1128/mSystems.00045-16

2015

  • Aylward F.O., L. Khadempour, D. Tremmel, B.R. McDonald, C.D. Nicora, S. Wu, and R.J. Moore, et al. 2015. "Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants." PLoS One 10, no. 8:e0134752. PNNL-SA-108498. doi:10.1371/journal.pone.0134752
  • Bernstein H.C., M.A. Charania, R.S. McClure, N.C. Sadler, M.R. Melnicki, E.A. Hill, and L.M. Markillie, et al. 2015. "Multi-omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142." Scientific Reports 5. PNNL-SA-111925. doi:10.1038/srep16004
  • Ream T.S., J.R. Haag, F. Pontvianne, C.D. Nicora, A.D. Norbeck, L. Pasa-Tolic, and C.S. Pikaard. 2015. "Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III- specific forms of the AC40 subunit, and alternative C53 subunits." Nucleic Acids Research 43, no. 8:4163-4178. PNNL-SA-108415. doi:10.1093/nar/gkv247
  • Sigdel T.K., Y. NG, S. Lee, C.D. Nicora, W. Qian, R.D. Smith, and D.G. Camp, et al. 2015. "Perturbations in the Urinary Exosome in Transplant Rejection." Frontiers of Medicine 1. PNNL-SA-106428. doi:10.3389/fmed.2014.00057
  • Touchette M.H., G.R. Bommineni, R.J. Delle Bovi, J. Gadbery, C.D. Nicora, A.K. Shukla, and J.E. Kyle, et al. 2015. "Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl ß-Diol Lipids." Biochemistry 54, no. 35:5457-5468. PNNL-SA-108635. doi:10.1021/acs.biochem.5b00455

2014

  • Aryal U.K., S.J. Callister, B.H. McMahon, L.A. McCue, J.N. Brown, J. Stockel, and M.L. Liberton, et al. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13, no. 7:3262-3276. PNNL-SA-102687. doi:10.1021/pr5000889
  • Brown J.N., H.M. Brewer, C.D. Nicora, K.K. Weitz, M.J. Morris, A.J. Skabelund, and J.N. Adkins, et al. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7. PNWD-SA-10347. doi:10.1186/1755-8794-7-58
  • Haag J.R., B. Brower-Toland, E.K. Krieger, L. Sidorenko, C.D. Nicora, A.D. Norbeck, and A. Irsigler, et al. 2014. "Functional Diversification of Maize RNA Polymerase IV and V subtypes via Alternative Catalytic Subunits." Cell Reports 9, no. 1:378-390. PNNL-SA-105690. doi:10.1016/j.celrep.2014.08.067
  • Huang E.L., F.O. Aylward, Y. Kim, B.M. Webb-Robertson, C.D. Nicora, Z. Hu, and T.O. Metz, et al. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6, no. 4:389-95. PNNL-SA-96938. doi:10.1111/1758-2229.12163
  • Mudenda L., S. Aguilar Pierle, J.E. Turse, G.A. Scoles, S.O. Purvine, C.D. Nicora, and T.R. Clauss, et al. 2014. "Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva." International Journal for Parasitology 44, no. 13:1029-1037. PNNL-SA-105510. doi:10.1016/j.ijpara.2014.07.003
  • Shi T., Y. Gao, M.J. Gaffrey, C.D. Nicora, T.L. Fillmore, W.B. Chrisler, and M.A. Gritsenko, et al. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87, no. 2:1103-1110. PNNL-SA-103421. doi:10.1021/ac503797x
  • Shi T., Y. Gao, S. Quek, T.L. Fillmore, C.D. Nicora, D. Su, and R. Zhao, et al. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13, no. 2:875-882. PNWD-SA-10119. doi:10.1021/pr400912c
  • Sigdel T.K., C.D. Nicora, S. Hsieh, H. Dai, W. Qian, D.G. Camp, and M.M. Sarwal. 2014. "Optimization for Peptide Sample Preparation for Urine Peptidomics." Clinical Proteomics 11. PNNL-SA-98818. doi:10.1186/1559-0275-11-7
  • Sigdel T.K., N. Salomonis, C.D. Nicora, S. Ryu, J. He, V. Dinh, and D.J. Orton, et al. 2014. "The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics." Molecular & Cellular Proteomics. MCP 13, no. 2:621-631. PNWD-SA-10124. doi:10.1074/mcp.M113.030577
  • Webb-Robertson B.M., M.M. Matzke, S. Datta, S.H. Payne, J. Kang, L.M. Bramer, and C.D. Nicora, et al. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13, no. 12:3639-3646. PNNL-SA-95335. doi:10.1074/mcp.M113.030932
  • Wrighton K.C., C. Castelle, M.J. Wilkins, L.A. Hug, I. Sharon, B.C. Thomas, and K.M. Handley, et al. 2014. "Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer." The ISME Journal 8, no. 7:1452-1463. PNNL-SA-97151. doi:10.1038/ismej.2013.249

2013

  • Aylward F.O., K.E. Burnum-Johnson, S.G. Tringe, C. Teiling, D. Tremmel, J. Moeller, and J.J. Scott, et al. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79, no. 12:3770-3778. PNNL-SA-92750. doi:10.1128/AEM.03833-12
  • D'haeseleer P., J.M. Gladden, M. Allgaier, P. Chain, S.G. Tringe, S. Malfatti, and J.T. Aldrich, et al. 2013. "Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass." PLoS One 8, no. 7:e68465. PNNL-SA-98320. doi:10.1371/journal.pone.0068465
  • DeAngelis K.M., D. Sharma, R. Varney, B.A. Simmons, N.G. Isern, L.M. Markillie, and C.D. Nicora, et al. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4. PNNL-SA-96504.
  • Isanapong J., S. Hambright, A.G. Willis, A. Boonmee, S.J. Callister, K.E. Burnum-Johnson, and L. Pasa-Tolic, et al. 2013. "Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium." The ISME Journal 7, no. 9:1803-1813. PNNL-SA-98615. doi:10.1038/ismej.2013.74
  • Nicora C.D., B.J. Anderson, S.J. Callister, A.D. Norbeck, S.O. Purvine, J.K. Jansson, and O.U. Mason, et al. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies." Proteomics 13, no. 18-19:2776-2785. PNNL-SA-92783. doi:10.1002/pmic.201300003
  • Robidart J.C., S.J. Callister, P.F. Song, C.D. Nicora, C.G. Wheat, and P.R. Girguis. 2013. "Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers." Environmental Science & Technology 47, no. 9:4399-4407. PNNL-SA-90834. doi:10.1021/es3037302
  • Shi T., T.L. Fillmore, Y. Gao, R. Zhao, J. He, A.A. Schepmoes, and C.D. Nicora, et al. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85, no. 19:9196-9203. PNNL-SA-96700. doi:10.1021/ac402105s
  • Wilkins M.J., K.C. Wrighton, C.D. Nicora, K.H. Williams, L.A. McCue, K.M. Handley, and C.S. Miller, et al. 2013. "Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface." PLoS One 8, no. 3:e57819. PNNL-SA-91270. doi:10.1371/journal.pone.0057819
  • Zhou J., R.K. Krovvidi, Y. Gao, H. Gao, B.O. Petritis, A. De, and C. Miller-Graziano, et al. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7, no. 7-8:571-583. PNWD-SA-9434. doi:10.1002/prca.201200109

2012

  • Aryal U.K., J. Stockel, E.A. Welsh, M.A. Gritsenko, C.D. Nicora, D.W. Koppenaal, and R.D. Smith, et al. 2012. "Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light." Journal of Proteome Research 11, no. 2:609-619. PNNL-SA-80375. doi:10.1021/pr200959x
  • Aylward F.O., K.E. Burnum, J.J. Scott, G. Suen, S.G. Tringe, S.M. Adams, and K.W. Barry, et al. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6, no. 9:1688-1701. PNNL-SA-82393. doi:10.1038/ismej.2012.10
  • Chauvigne-Hines L.M., L.N. Anderson, H.M. Weaver, J.N. Brown, P.K. Koech, C.D. Nicora, and B.A. Hofstad, et al. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134, no. 50:20521-20532. PNNL-SA-91066. doi:10.1021/ja309790w
  • Chauvin T., F. Xie, T. Liu, C.D. Nicora, F. Yang, D.G. Camp, and R.D. Smith, et al. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87, no. 6:Article No. 141. PNNL-SA-90200. doi:10.1095/biolreprod.112.104208
  • Haag J.R., T.S. Ream, M. Marasco, C.D. Nicora, A.D. Norbeck, L. Pasa-Tolic, and C.S. Pikaard. 2012. "In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing." Molecular Cell 48, no. 5:811-8. PNNL-SA-90501. doi:10.1016/j.molcel.2012.09.027
  • Zhou J., G.P. Dann, T. Shi, L. Wang, X. Gao, D. Su, and C.D. Nicora, et al. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84, no. 6:2862-2867. PNNL-SA-84751. doi:10.1021/ac203394r

2011

  • Burnum K.E., S.J. Callister, C.D. Nicora, S.O. Purvine, P. Hugenholtz, F. Warnecke, and R.H. Scheffrahn, et al. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5, no. 1:161-164. PNNL-SA-68831. doi:10.1038/ismej.2010.97
  • Parnell J.J., S.J. Callister, G. Rompato, C.D. Nicora, L. Pasa-Tolic, A. Williamson, and M.E. Pfrender. 2011. "Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock." Scientific Reports 1. PNNL-SA-74290. doi:10.1038/srep00025
  • Qian W., B.O. Petritis, C.D. Nicora, and R.D. Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." In Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, edited by K Gevaert and J Vandekerckhove. 43-54. Totowa, New Jersey:Humana Press Inc. PNNL-SA-78931.
  • Stockel J., J.M. Jacobs, T.R. Elvitigala, M.L. Liberton, E.A. Welsh, A.D. Polpitiya, and M.A. Gritsenko, et al. 2011. "Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142." PLoS One 6, no. 2:Article No.: e16680. PNNL-SA-78209. doi:10.1371/journal.pone.0016680
  • Wilkins M.J., S.J. Callister, M. Miletto, K.H. Williams, C.D. Nicora, D.R. Lovely, and P.E. Long, et al. 2011. "Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)." Microbial Biotechnology 4, no. 1:55-63. PNNL-SA-72264. doi:10.1111/j.1751-7915.2010.00194.x

2010

  • Angel T.E., B.J. Luft, X. Yang, C.D. Nicora, D.G. Camp, J.M. Jacobs, and R.D. Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5, no. 11:Article No.: e13800. PNNL-SA-74148. doi:10.1371/journal.pone.0013800
  • Callister S.J., M.J. Wilkins, C.D. Nicora, K.H. Williams, J.F. Banfield, N. VerBerkmoes, and R.L. Hettich, et al. 2010. "Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles." Environmental Science & Technology 44, no. 23:8897-8903. PNNL-SA-71892. doi:10.1021/es101029f
  • Smith D.P., J.B. Kitner, A.D. Norbeck, T.R. Clauss, M.S. Lipton, M.S. Schwalbach, and L. Steindler, et al. 2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5, no. 5:Article Number: e10487. PNNL-SA-72424.

2009

  • Henne K.L., J.E. Turse, C.D. Nicora, M.S. Lipton, S.L. Tollaksen, C. Lindberg, and G. Babbnig, et al. 2009. "Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24." Journal of Proteome Research 8, no. 4)(Sp.Iss.SI:1704-16. PNNL-SA-62660. doi:10.1021/Pr800705f
  • Kim W., M.W. Silby, S.O. Purvine, J.S. Nicoll, K.K. Hixson, M.E. Monroe, and C.D. Nicora, et al. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4, no. 12:Article Number: e8455. PNNL-SA-68830. doi:10.1371/journal.pone.0008455
  • Ream T.S., J.R. Haag, A.T. Wierzbicki, C.D. Nicora, A.D. Norbeck, J. Zhu, and G. Hagen, et al. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II." Molecular Cell 33, no. 2:192-203. PNNL-SA-75446. doi:10.1016/j.molcel.2008.12.015
  • Ream T.S., J.R. Haag, A.T. Wierzbicki, C.D. Nicora, A.D. Norbeck, J.K. Zhu, and G. Hagen, et al. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II." Molecular Cell 33, no. 2:192-203. PNNL-SA-62481. doi:doi:10.1016/j.molcel.2008.12.015
  • Sowell S.M., L. Wilhelm, A.D. Norbeck, M.S. Lipton, C.D. Nicora, D.F. Barofsky, and C. carlson, et al. 2009. "Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3, no. 1:93-105. PNNL-SA-60995.
  • Wilkins M.J., N.C. VerBerkmoes, K.H. Williams, S.J. Callister, P. Mouser, H. Elifantz, and A.L. N'Guessan, et al. 2009. "Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation." Applied and Environmental Microbiology 75, no. 20:6591-6599. PNNL-SA-68828. doi:10.1128/AEM.01064-09

2008

  • Sowell S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, and D.F. Barofsky, et al. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74, no. 13:4091-4100. PNNL-SA-114147. doi:10.1128/AEM.00599-08
  • Sowell S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, and D.F. Barofsky, et al. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74, no. 13:4091-4100. PNNL-SA-59403. doi:10.1128/AEM.00599-08

2006

  • Callister S.J., C.D. Nicora, X. Zeng, J. Roh, M. Dominguez, C. Tavano, and M.E. Monroe, et al. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67, no. 3:424-436. PNNL-SA-46423. doi:10.1016/j.mimet.2006.04.021
  • Callister S.J., M. Dominguez, C.D. Nicora, X. Zeng, C. Tavano, S. Kaplan, and T. Donohue, et al. 2006. "Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1 Aerobic and Photosynthetic Cell Cultures." Journal of Proteome Research 5, no. 8:1940-1947. PNNL-SA-48567.
  • Fang R., D.A. Elias, M.E. Monroe, Y. Shen, M. McIntosh, P. Wang, and C.D. Goddard, et al. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5, no. 4:714-725. PNNL-SA-47983. doi:10.1074/mcp.M500301-MCP200
  • Yang F., D.L. Stenoien, E.F. Strittmatter, J. Wang, L. Ding, M.S. Lipton, and M.E. Monroe, et al. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation." Journal of Proteome Research 5, no. 5:1252-1260. PNNL-SA-46275.

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